micom allows you to construct a community model from a list on input
COBRA models and manages exchange fluxes between individuals and individuals
with the environment. It explicitly accounts for different abundances of
individuals in the community and can thus incorporate data from 16S rRNA
sequencing experiments. It allows optimization with a variety of algorithms
modeling the trade-off between egoistic growth rate maximization and
cooperative objectives.

Attribution

Micom is described in a recent preprint that you can cite.
If you have any questions contact us at oresendis (at) inmegen.gob.mx. Thanks 😄